Abstract Efficient and reproducible detection of immune cell states is paramount to our understanding of the immune responses in the context of health and disease, such as cancer and autoimmunity. This service core provides capabilities and a pipeline for the preparation, sequencing and basic analysis of RNA. This experimental and computational resource will facilitate investigations of immunity in EAE mice that are deficient for TIGIT, PD1 or both, the characterization of cells isolated from human biopsies or blood from patients with multiple sclerosis or glioma, and the analysis of in vitro stimulated cells expressing TIGIT and/or PD-1 in Projects 1-3. The Core leverages the strengths of the Love Lab at MIT with expertise in bulk RNA-sequencing and the Shalek Lab at MIT with advanced approaches for single-cell RNA-sequencing. To facilitate the objectives of the three Projects, two services will be provided: RNA-sequencing of bulk populations of cells, and single-cell RNA- sequencing (scRNA-Seq). For the latter, methods for plate-based (96- or 384-well) sequencing will be available, as well as a novel method developed by Investigators Shalek and Love called Seq-Well that allows sequencing of 1,000?s of single cells in parallel in a manner similar to reported Drop-Seq methods. Another aspect will be the capability to recover the T cell receptors from single cells. Together these analytical capabilities in this Core will further the objectives of the Program by making deep immunological characterization with single-cell resolution available for each of the Projects.